However, the government is not legally bound by the vote and could still press on regardless.

The shadow environment secretary, Mary Creagh, said after the debate: “The government should now come clean with the public and farmers and declare that the cull will not now go ahead. It is not fair for farmers to be strung along, and the public have shown that they will not accept a badger cull.”

David Heath, the Liberal MP for Somerton and Frome, who is also thefarming minister, made a forceful defence of the cull during the debate.

He said: “We cannot afford to shy away from tackling the rampant spread of TB throughout our cattle herds. None of [the opponents] – not the critics, not scientists, not politicians – have come up with a single workable alternative to the cull which would give us the positive impact we need right now.”

The environment secretary, Owen Paterson, was present for 20 minutes of the five-hour debate. Several Labour MPs reported that he said “I can’t stand any more of this” as he walked out of the discussion.

Paterson said later: “I didn’t storm in or out anywhere. As I left I might have joked about the ill-informed comments of the other side.”

During the debate, Sir Jim Paice, who lost the farming minister’s post in September’s reshuffle, said that he and other ministers were under “special security measures due to threats from animal-rights extremists”.

He also commented on the shooting of free-running badgers. The killing method marked a key difference between the government’s proposals and the evidence arising from a landmark £50m, 10-year culling trial, in which 11,000 badgers were captured in cages then shot with pistols.

Paice said: “Nobody knows if controlled shooting will cull 70% of badgers [the minimum required] or be humane. There is no science, I readily admit that, because it has never been done.”

He said that the now-postponed pilot culls in Somerset and Gloucestershire had to go ahead to “test free shooting”.

The lost vote means a problem for ministers if they decide to push on with the cull, as they risk being accused of ignoring the will of parliament.

On Wednesday, the attorney general, Dominic Grieve, said “parliament is sovereign” in the matter of whether the European court of human rights could force the UK to give prisoners the vote. Ministers would need to argue that parliament was not sovereign in the case of the badger cull, or possibly call another vote and whip MPs hard to ensure a victory.

Before the vote, Heath was asked by Tory MP Mark Pritchard: “Will ministers accept the will of this house?” Heath said they would “listen” to the views of the house.

Opponents of the cull welcomed the government defeat. Mark Jones at Humane Society International said: “The government has refused to listen to the majority of scientists, disease experts and the British people opposed to the cull. Surely now it must listen to the will of the parliament and abandon its policy for good … and stop wasting time and money on a politically motivated badger hunt.”

Gavin Grant, chief executive of the RSPB, said: “We stand ready to play a full part in working with farmers, land owners, the government and conservationists to move forward rapidly and constructively to tackle this dire disease in cattle and wildlife [using vaccination].”

Pat Hayden, vice-chair of the trust, expressed deep disappointment but said: “How we feel is much less important than the impact on the species we exist to protect. We owe it to our members to do our utmost to protect badgers.” The trust is now considering an appeal.

“We are pleased with the judgment,” said a spokesman for the Department for Environment, Food and Rural Affairs (Defra). “No one wants to cull badgers but in 2011 bovine TB led to the slaughter of over 26,000 cattle and to help eradicate the disease it needs to be tackled in badgers. We will continue to work with the farming industry so badger control in two pilot areas can start as soon as is practical.”

The judicial review considered only legal arguments, not scientific ones. In the course of the hearing, the government accepted that a landmark decade-long trial had shown that fleeing badgers carried TB to new areas. That trial found that, at best, TB incidence was reduced in the cull area by just 16% after nine years. The government also accepted the culls could cost farmers more than doing nothing.

David Williams, the chairman of the trust, said: “The Badger Trust emphatically did not ask the court to adjudicate on the science around culling. That remains exactly the same as it has been for a decade. Despite a constant stream of evidence that culling will make matters worse and growing consternation from many farmers, the coalition government intends to press ahead with its expensive and pointless policy.”

Martin Haworth, NFU director of policy, said: “Given the public interest in this issue, we always knew that there would be a legal challenge. We are pleased the judge has ruled that Defra’s approach is lawful. This policy is desperately needed to tackle what is a terrible and damaging disease that affects cattle and badgers and brings misery to the lives of many hard working farming families.”

In court, the Badger Trust’s legal team had argued that the cull would break the 1992 law protecting badgers, which only allows culling to “prevent the spread of disease”. The trust’s lawyers also argued that the cost-impact assessment of the environment secretary, Caroline Spelman, was flawed as it was based on shooting free-running badgers, rather than the far more expensive method used in the decade-long trial of trapping the animals in cages first. But Kate Grange, of the government legal team, told the court: “[Mr Justice Ouseley] has rejected the application in clear and robust terms.”

The trust now has seven days to seek leave for an appeal, a shorter period than the usual 21 days. Grange said: “Given where we are with the pilots, that is not unreasonable.”

The Badger Trust said in a statement: “The judgment demonstrates that the legislation in this area has not kept pace with developments in the understanding of how TB works.”

The RSPCA‘s David Bowles said: “We are bitterly disappointed. We believe culling is not a long-term, sustainable solution. It is not as if there aren’t alternatives to a cull. Vaccination could be more effective and sustainable.”

A badger vaccination programme is replacing a planned cull in Wales, following legal challenges and the election of a new political administration. Vaccination is being tested by the National Trust in Devonand by the Wildlife Trust in Gloucestershire. The previous Labour government said an oral badger vaccine would be ready by 2015. The coalition cancelled five of the six trials of injectable vaccines and Spelman says a useable oral vaccine is “years away”.

The government is also facing a complaint at the Council of Europe from the Humane Society International (HSI), which argues the badger cull contravenes the Bern Convention that protects wildlife. Mark Jones, veterinarian and executive director of HSI said: “This may now be the badgers’ last hope and we are determined to do everything we can to prevent this bloody and pointless slaughter.”

The Badger Trust, RSPCA, the League against Cruel Sports and other groups will hold public meetings in the next week to discuss the cull at Taunton and Tewkesbury, both towns in the two pilot areas.

• The original version of this story wrongly stated a pilot cull was planned for Devon, not Somerset.

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The badger is back in the news, and not because it’s loved… The counties for the planned cull have now been revealed – see my Learn From Nature blog

Below … the badger goes to court!

The battle for the badger has begun in earnest, with the opening shot of a high court legal battle being fired, a complaint made under European wildlife law and a new public opinion poll showing just 12% of people think killing badgers should be the main focus in attempting to reduce the spread of tuberculosis in cattle.

How did it get to this? Pretty easily. The government was under severe pressure to tackle what is truly a terrible problem for infected herds – they have to be slaughtered at great financial and emotional cost to farmers and to the taxpayer, who paid £90m in compensation for the 25,000 cattle killed in 2010. Environment secretary Caroline Spelman had a world-class scientific trial, conducted over 10 years, on her desk showing that persistent culling of badgers over a decade can cut bovine TB by about 16%.

So far so good. But to expand the cull using the trap-and-shoot method of killing employed in the trial would be even more expensive than doing nothing. So the government gave the go-ahead for the cull using “free-shooting” – a man in a tree with a high-powered rifle. At this point, the “science-led” tag Spelman used to justify the go-ahead disappeared in a puff of gun-smoke, and that’s not just me saying it but lots of the scientists who ran the 10-year-trial.

There will be a tiny trial of free-shooting, but if it is shown to be ineffective, the whole cull is fatally wounded. That’s one of the three legal grounds the Badger Trust is using to seek a judicial review in the high court of Spelman’s decision. As it happens, even if free-shooting is judged acceptable, the government’s own impact assessment shows the culls will still be more expensive for farmers than doing nothing and taking the hit – hideous as that is – of TB infection. And that’s without accounting for the legal challenges and the high costs of policing shooter-versus-activists stand-offs in the woods at night.

What does the public think? A new poll, published on Tuesday, shows us that 31% support the cull, 40% oppose it and a lot of people – 29% – don’t know. The poll was a professional one, run by YouGov, for the animal protection charity Humane Society International (HSI), whose UK director Mark Jones said: “The majority of the public oppose killing badgers, but the poll also indicates a significant level of indecision or confusion and I suspect that this stems from uncertainty surrounding the issue of whether or not a cull is ‘science-led’. Defra has consistently claimed that its cull policy would be science-led and yet the scientific legitimacy of culling badgers has been vociferously questioned by highly respected scientists and conservationists such as Lord Krebs [who led the 10-year trial] and Sir David Attenborough.”

YouGov also asked people what they though should be the main tool for dealing with bovine TB. Culling was backed by 12%, as was restricting cattle movements and reforming farm practices, and 15% didn’t know. But the most popular choice by far was vaccination, which was backed by 60% of people in England.

Vaccination programmes are taking place right now and trapping and injecting badgers is expensive, though it can hardly cost much more than trapping and shooting them. Back in 2010, the previous government said an oral vaccine would be ready by 2015, which could be left in bait, a much cheaper way to innoculate the animals.

But the new coalition government cancelled five of the six vaccination trials set up. Spelman now says a useable vaccine is “years away”, which certainly helps bolster the case for shooting badgers, if not pleasing the English public. I estimate the cull will cost £92m, plus legal and policing costs, over eight years, while vaccination research is getting just £20m.

HSI has also brought a complaint against Spelman via the Bern Convention, which binds the UK government to regulate any exploitation of badgers to keep populations “out of danger”, unless certain conditions are met.

So, we have a “science-led” cull disowned by the researchers who led the science and one that will cost more than doing nothing. Everyone’s first choice – vaccination- has lost funding, and the row is now in the expensive realm of the courts. This is not on track to end well for badgers, cattle, farmers, scientists or the taxpayer.

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Can nobody stop it? Can no major political leader or other public figure realise what is happening and have the guts or find a moment to speak out about the horrific, heartless, headlong slaughter of the world’s rhinos which is now running out of control?

Yes of course, most people naturally have concerns at the moment which preclude worrying about the welfare of wildlife. But the rhino carnage now going on is different; in its scale, it is something quite new. Driven by an urban myth in Asia – that a Vietnamese politician had his liver cancer cured by powered rhino horn – the price of horn has shot up to about $38,000 per kilo, more than the price of cocaine, and approaching the price of gold. These lumberingly gentle, charismatic animals might as well be walking around with a solid gold nose, and as a result are being butchered as never before.

Last week I wrote about the fact that Vietnam’s own rhino, a subspecies of the Javan rhinoceros only discovered in 1988, had been wiped out by poachers for the traditional Asian medicine trade in a mere two decades, and suggested that this should make us think hard about ourselves as a species and our killer tendencies.

On the very day I wrote this, the world wildlife watchdog, the International Union for the Conservation of Nature, announced that a further rhino subspecies, the western black rhino from West Africa, had also been driven extinct, while a third, the northern white rhino, last seen in the Democratic Republic of the Congo, had “probably” been driven over the edge. In addition to that, the IUCN said, the Javan rhinoceros itself is teetering on the brink, probably down to about 40 individuals, in a single park in Indonesia.

In South Africa, a poaching war is in full swing now in supposed sanctuaries like the Kruger National Park; by the end of August, nearly 300 animals had been killed for their horn in South Africa this year alone and the final total will be much higher, probably more than 400 (between 2000 and 2007 it averaged 12). Even in Britain we are feeling the effects: several museums have been broken into and have had antique trophy rhino heads stolen for the horn.

Now comes even more disturbing news: a report from the Humane Society International, complete with sickening photographs, reveals that the latest trend is for poachers to use silent tranquiliser dart guns, rather than rifles, as the risk of detection by wildlife protection officials is less. So while the animals are still alive, the HSI report says, the poachers “use machetes and chainsaws to hack off their horns, leaving the animals to regain consciousness with hideous deep face wounds, massive blood loss and unimaginable pain”.

The executive director of HSI, Mark Jones, himself a vet, says: “The rhinos who die whilst still anaesthetised are the lucky ones.”

And all this for a myth. All this for the fable, long accepted in traditional Asian medicine, that rhino horn has curative properties. In fact, rhino horn is largely composed of keratin, the substance of which our fingernails and hair are made, and has no medicinal properties whatsoever. But the burgeoning Asian middle classes – those for whom traditional medicine is a way of life – have now gone from an ancient belief that the horn cures fevers, to believing that horn cures cancer, and are bidding the price up to spectacular and disastrous levels.

To its credit, the British Government three months ago began an initial protest about the situation, and at a committee meeting of the Convention on International Trade in Endangered Species (Cites) put forward a request – on behalf of the whole European Union – for Asian nations to mount awareness-raising campaigns, pointing out rhino horn’s non-existent medicinal virtues. There is a sensitivity about seeming to interfere in the internal affairs of countries like China and Vietnam, but Richard Benyon, the UK Wildlife minister, said: “The world community cannot sit back and just watch these species disappear.”

Yet disappearing they are. Of the five main rhinoceros species, all except one – the population of white rhinos in South Africa – are now threatened with extinction. It is happening before our eyes. These marvellous relicts of the age of megafauna, of the time of the mammoth and sabre-toothed tiger and other remarkable beasts which died out at the close of the last ice age, are coming to the end of their time on Earth, simply through naked human greed.

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Hidden agenda? A very interesting development is reported by The Independent : Evidence of overwhelming public opposition to the proposed cull of badgers was withheld until the Government had decided to go ahead with the controversial plan.

The results of a consultation held last year revealed that 69 per cent of respondents were against killing up to hundreds of thousands of the mammals in a bid to eradicate tuberculosis from cattle herds in England.

Scientific experts, animal-welfare organisations and wildlife groups objected to the proposal which was announced by the Environment Secretary Caroline Spelman in the House of Commons earlier this month.

The consultation, which was completed in December 2010, was eventually – and discreetly – published on a Government website on the day of the much-anticipated statement following a request under the Freedom of Information Act from the Humane Society International (HSI).

A spokesman for the Department for Environment, Food and Rural Affairs (Defra) insisted it was “entirely normal” to publish consultation responses at the same time as policy proposals.

Under the scheme, syndicates of farmers are expected to be given the go-ahead to shoot badgers in the hope of limiting the spread of the disease, which resulted in the slaughter of 25,000 cattle last year, costing taxpayers £90m.

The policy is backed by the National Farmers Union, landowners and vets. Culling could begin as early as next spring in the West and South-west – the worst-affected parts of the country – potentially sparking clashes between animal-rights activists and teams of shooters. A legal challenge looks almost certain.

Among the nearly 60,000 responses were submissions from the Independent Scientific Group on Cattle TB, which completed a random badger-culling trial in 2007. It challenged Defra’s claim that a 16 per cent reduction in bovine TB could be achieved over nine years through farm-based culling.

The wildlife expert and television presenter Bill Oddie said either the Government did not understand the environmental issues or did not care for public opinion. “Time and again in recent years, responsible and authoritative research has concluded that a cull will not prevent cattle from contracting TB, and indeed that it could make the situation worse,” he said.

Sixty-one per cent opposed culling, but said they would consider vaccination of the badger population; 8 per cent said they wanted neither of the options, while just under one-third of respondents were in favour of both vaccination and shooting.

Ms Spelman said an approved cattle and an oral badger vaccine were still “much further away than we thought”. Mark Jones, director of HSI, said the policy had been formulated by ministers concerned with “pacifying a misguided minority of their rural constituents”. He added: “Animal injury, suffering and death will once again become commonplace in our countryside, in the mistaken belief that it will somehow alleviate the financial burden created by a livestock disease problem initiated and spread by poor agricultural practices.”

Defra said a final decision on the cull had not yet been reached and that the Government would be carrying out a second consultation later this year.

Battle lines for a countryside conflict were drawn up yesterday after the Government said it would permit a cull of badgers in a bid to limit the spread of TB in cattle. The Independent reports on a ‘black day’ – this blog writer’s opinion.

Opposition politicians, animal welfare organisations and wildlife groups queued up to criticise the plans, announced by the Environment Secretary, Caroline Spelman, as inhumane, unscientific and unnecessary, while farmers, landowners and vets welcomed them as essential in the fight against the disease.

The split foreshadows an almost certain legal challenge to the proposals, likely to come into effect next year, and the possibility of violent disorder if attempts are made by animal rights activists and others to prevent a cull.

Subject to successful trials next summer, groups of farmers will be licensed to organise the widespread shooting of badgers across England, Mrs Spelman told the Commons. She said it was clear that badgers were contributing to the spread of TB among cattle and current measures were not checking it.

“This terrible disease saw 25,000 cattle slaughtered last year, has cost taxpayers £500m over the last 10 years in England alone, and if not checked, will cost a billion pounds over the next decade,” she said, commenting that she was “persuaded of the case for culling”.

Under the plans, farmers will be allowed to come together in syndicates to organise culls, at their own expense, over substantial areas of at least 150 squares kilometres, and lasting at least four years. The aim will be to cull at least 70 per cent of the badgers in a given area; the killing will be done by specially trained marksmen with high-powered rifles.

After further discussions on the licensing arrangements over the next few weeks, two pilot schemes next summer will test that the shooting method is effective, humane and safe for the public, and if it is given the go-ahead by an independent panel, widespread culling could begin next year or possibly in 2013.

Mary Creagh, Shadow Environment Secretary, said that the cull was “the wrong way to tackle bovine TB“. She said: “This decision is driven by political expediency rather than sound science. Free shooting of badgers has never been tested and could prove inhumane. The cull will cost farmers more than it saves them, and could spread bovine TB in the short term as badgers move out of cull areas.”

Caroline Lucas, leader of the Green Party, spoke of “a barbaric slaughter of badgers”. The RSPCA said the decision marked “a black day”, and the League Against Cruel Sports said that “all the evidence shows that culls do not work”.

The Humane Society International said it was “appalled” by the decision. “The slaughter of badgers as a means of controlling the spread of tuberculosis in cattle has been overwhelmingly declared ineffective by a host of eminent scientific experts,” said director Mark Jones. “We do not need further government consultations, pilot studies or trials to tell us that slaughtering badgers won’t help.”

Peter Kendall, president of the National Farmers’ Union, said: “I join with farmers up and down the country today in breathing an enormous sigh of relief that the Government has shown leadership in tackling this terrible disease. This has never been about eradicating badgers; this is about eradicating disease. Today is a massive step forward.